3GZJ

Crystal Structure of Polyneuridine Aldehyde Esterase Complexed with 16-epi-Vellosimine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WFL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	296	PEG 3350, 0.20M Bis-Tris, 0.25M Lis2SO4, pH 6.3, vapor diffusion, hanging drop, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.21	α = 90
b = 44.61	β = 104.44
c = 180.41	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	PSI PILATUS 6M		2007-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.19	20	97.2	0.077	0.077	10.9	3.2	66881	66881			44.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.19	2.32	93.9		0.425	0.425	2.2	3	10364

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2WFL	2.19	20	66881	66881	3407	97.19	0.212	0.212	0.209	0.278	RANDOM	27.852

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-2.05		0.61	3.26		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.778
r_dihedral_angle_3_deg	18.159
r_dihedral_angle_4_deg	16.221
r_dihedral_angle_1_deg	6.814
r_scangle_it	3.613
r_scbond_it	2.491
r_angle_refined_deg	1.841
r_mcangle_it	1.427
r_mcbond_it	0.923
r_symmetry_vdw_refined	0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.778
r_dihedral_angle_3_deg	18.159
r_dihedral_angle_4_deg	16.221
r_dihedral_angle_1_deg	6.814
r_scangle_it	3.613
r_scbond_it	2.491
r_angle_refined_deg	1.841
r_mcangle_it	1.427
r_mcbond_it	0.923
r_symmetry_vdw_refined	0.36
r_symmetry_hbond_refined	0.337
r_nbtor_refined	0.316
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.128
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9985
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	88

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.